J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W186-92. doi: 10.1093/nar/gks528. Epub 2012 Jun 4.
A gene prediction program, VIGOR (Viral Genome ORF Reader), was developed at J. Craig Venter Institute in 2010 and has been successfully performing gene calling in coronavirus, influenza, rhinovirus and rotavirus for projects at the Genome Sequencing Center for Infectious Diseases. VIGOR uses sequence similarity search against custom protein databases to identify protein coding regions, start and stop codons and other gene features. Ribonucleicacid editing and other features are accurately identified based on sequence similarity and signature residues. VIGOR produces four output files: a gene prediction file, a complementary DNA file, an alignment file, and a gene feature table file. The gene feature table can be used to create GenBank submission. VIGOR takes a single input: viral genomic sequences in FASTA format. VIGOR has been extended to predict genes for 12 viruses: measles virus, mumps virus, rubella virus, respiratory syncytial virus, alphavirus and Venezuelan equine encephalitis virus, norovirus, metapneumovirus, yellow fever virus, Japanese encephalitis virus, parainfluenza virus and Sendai virus. VIGOR accurately detects the complex gene features like ribonucleicacid editing, stop codon leakage and ribosomal shunting. Precisely identifying the mat_peptide cleavage for some viruses is a built-in feature of VIGOR. The gene predictions for these viruses have been evaluated by testing from 27 to 240 genomes from GenBank.
一种基因预测程序 VIGOR（病毒基因组 ORF 读取器）于 2010 年在 J. 克雷格·文特尔研究所开发，已成功用于冠状病毒、流感病毒、鼻病毒和轮状病毒的基因调用，为传染病基因组测序中心的项目提供服务。VIGOR 使用序列相似性搜索针对自定义蛋白质数据库来识别蛋白质编码区域、起始和终止密码子以及其他基因特征。基于序列相似性和特征残基，准确识别核糖核酸编辑和其他特征。VIGOR 生成四个输出文件：基因预测文件、互补 DNA 文件、对齐文件和基因特征表文件。基因特征表可用于创建 GenBank 提交。VIGOR 只需一个输入：FASTA 格式的病毒基因组序列。VIGOR 已扩展到预测 12 种病毒的基因：麻疹病毒、腮腺炎病毒、风疹病毒、呼吸道合胞病毒、甲病毒和委内瑞拉马脑炎病毒、诺如病毒、肺炎支原体病毒、黄热病病毒、日本脑炎病毒、副流感病毒和仙台病毒。VIGOR 准确检测核糖核酸编辑、终止密码子渗漏和核糖体移位等复杂基因特征。VIGOR 的一个内置功能是准确识别某些病毒的 mat_peptide 切割。通过从 GenBank 测试 27 到 240 个基因组，对这些病毒的基因预测进行了评估。
